my wife's H1B expire in Sep , Her PERM is applied and submitted after 6 year, so can not renew now.

Your wife can change to H-4 as that does not count against the 6 years. When the I-140 petition is approved, she can apply for H-1B change of status. If she is out of the country, she can apply for H-1B petition, pointing out that the I-140 petition is already been approved. Once the petition is approved, she would then be processed for H-1B visa by either an American consulate or embassy if she requires a visa or entry if Canadian by Customs and Border Protection (CBP). Due to the limitations of the Lawyers.com Forums, Alan Lee, Esq.'s (the "Firm") participation in responding to questions posted herein does not constitute legal advice, nor legal representation of the person or entity posting a question. No Attorney/Client relationship is or shall be construed to be created hereby. The information provided herein by the Firm is general, and requires that the poster obtain specific legal advice from an attorney. The poster shall not rely upon the information provided herein as legal advice nor as the basis for making any decisions of legal consequence  

In answering your earlier version of this question (which you clarified), I failed to address her leaving the country.  If she leaves, she can come back as an H4 if you are still in H1 status, and she can come back as an immigrant if her I-140 has been approved by the time she returns.